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7 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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LRFN3
leucine rich repeat and fibronectin type III domain containing 3
Chromosome 19 · 19q13.12
NCBI Gene: 79414Ensembl: ENSG00000126243.9HGNC: HGNC:28370UniProt: Q9BTN0
13PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
presynaptic active zone membranecell surfaceplasma membranepostsynaptic density membrane46,XX testicular disorder of sex developmentazoospermia46,XY complete gonadal dysgenesis46,XY disorder of sex development due to 5-alpha-reductase 2 deficiency
✦AI Summary

LRFN3 (leucine rich repeat and fibronectin type III domain containing 3) is a neuronal transmembrane glycoprotein belonging to the LRR-Ig-Fn superfamily of cell adhesion molecules. It mediates homophilic, calcium-independent cell-cell adhesion and promotes neurite outgrowth in hippocampal neurons. LRFN3 contains leucine-rich repeat, immunoglobulin-like, and fibronectin type III domains, with an extracellular N-terminus and intracellular C-terminus that can bind PDZ domains of postsynaptic scaffolding proteins like PSD95, suggesting a role in synaptic organization 1. The gene is predominantly expressed in the adult mouse and human brain, with expression initiated during immature neural cell development 1. Beyond its canonical neuronal functions, LRFN3 has emerged as a candidate gene in several disease contexts. It harbors a neoantigen mutation (R118Q) that induced heightened neoantigen-reactive T cell responses in colorectal cancer patients, with potential immunotherapeutic applications 2. LRFN3 shows frequent chr19 gains in embryonal rhabdomyosarcoma, suggesting a role in sarcoma pathogenesis 3. Additionally, LRFN3 carries multiple genetic variants associated with opioid use disorder, functioning within calcium signaling and opioid addiction pathways 4. Recent evidence links LRFN3 to inflammatory bowel disease susceptibility through ancestry-specific African alleles 5, and to rheumatoid arthritis via glycolysis-related gene networks 6. These findings indicate LRFN3's broader involvement in immune-mediated and metabolic disease pathogenesis beyond its primary neurobiological function.

Sources cited
1
LRFN3 is a neuronal transmembrane glycoprotein with LRR-Ig-Fn domain structure, expressed predominantly in adult brain, mediates cell adhesion, and binds PSD95
PMID: 16828986
2
LRFN3-R118Q is a neoantigen mutation that induces heightened neoantigen-reactive T cell responses in colorectal cancer
PMID: 33689574
3
LRFN3 shows frequent chromosomal gains at 19q13.12 in embryonal rhabdomyosarcoma
PMID: 24551291
4
LRFN3 harbors multiple genetic variants in opioid use disorder cases and participates in calcium signaling and opioid addiction pathways
PMID: 39684228
5
LRFN3 is associated with African-ancestry-specific inflammatory bowel disease risk alleles
PMID: 41661118
6
LRFN3 is identified as a glycolysis-related candidate gene for rheumatoid arthritis through multi-omics analysis
PMID: 41693713
Disease Associationsⓘ20
46,XX testicular disorder of sex developmentOpen Targets
0.06Suggestive
azoospermiaOpen Targets
0.06Suggestive
46,XY complete gonadal dysgenesisOpen Targets
0.06Suggestive
46,XY disorder of sex development due to 5-alpha-reductase 2 deficiencyOpen Targets
0.05Suggestive
46,XX ovotesticular disorder of sex developmentOpen Targets
0.05Suggestive
hypogonadotropic hypogonadism 11 with or without anosmiaOpen Targets
0.05Suggestive
familial male-limited precocious pubertyOpen Targets
0.05Suggestive
Testicular regression syndromeOpen Targets
0.05Suggestive
cryptorchidismOpen Targets
0.05Suggestive
spermatogenic failure 71Open Targets
0.05Suggestive
spermatogenic failure, X-linked, 2Open Targets
0.05Suggestive
partial chromosome Y deletionOpen Targets
0.04Suggestive
X-linked intellectual disability - macrocephaly - macroorchidismOpen Targets
0.04Suggestive
X-linked intellectual disability-macrocephaly-macroorchidism syndromeOpen Targets
0.04Suggestive
hypogonadotropic hypogonadism 14 with or without anosmiaOpen Targets
0.04Suggestive
46,XY disorder of sex development due to isolated 17,20 lyase deficiencyOpen Targets
0.04Suggestive
familial adrenal hypoplasia with absent pituitary luteinizing hormoneOpen Targets
0.04Suggestive
spinocerebellar ataxia type 32Open Targets
0.04Suggestive
testicular agenesisOpen Targets
0.04Suggestive
persistent Mullerian duct syndromeOpen Targets
0.04Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
PTPRFProtein interaction77%FLOT1Protein interaction77%DLG4Protein interaction75%PTPRSProtein interaction72%FLOT2Protein interaction71%LRFN4Shared pathway67%
Tissue Expression6 tissues
Ovary
100%
Liver
68%
Lung
44%
Brain
42%
Heart
25%
Bone Marrow
2%
Gene Interaction Network
Click a node to explore
LRFN3PTPRFFLOT1DLG4PTPRSFLOT2LRFN4
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9BTN0
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.10LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.67 [0.42–1.10]
RankingsWhere LRFN3 stands among ~20K protein-coding genes
  • #16,209of 20,598
    Most Researched13
  • #11,266of 17,882
    Most Constrained (LOEUF)1.10
Genes detectedLRFN3
Sources retrieved7 papers
Response time—
📄 Sources
7▼
1
Neoantigen-reactive T cells exhibit effective anti-tumor activity against colorectal cancer.
PMID: 33689574
Hum Vaccin Immunother · 2022
1.00
2
Comparative analysis of structure, expression and PSD95-binding capacity of Lrfn, a novel family of neuronal transmembrane proteins.
PMID: 16828986
Gene · 2006
0.86
3
Chromosomal and genetic imbalances in Chinese patients with rhabdomyosarcoma detected by high-resolution array comparative genomic hybridization.
PMID: 24551291
Int J Clin Exp Pathol · 2014
0.71
4
Genetic Variants Linked to Opioid Addiction: A Genome-Wide Association Study.
PMID: 39684228
Int J Mol Sci · 2024
0.57
5
Genomic Insights Into Inflammatory Bowel Disease in United States Hispanic Participants: An Ancestry-Focused Study.
PMID: 41661118
Gastroenterology · 2026
0.43